If my theory is correct, you've done the best thing you could have done, however, if there are any others out there with similiar problems, replacing the speakers may not have been "necessary". That being said, aftermarket speakers are definately leaps and bounds better than factory.
I would say since all the speakers quit working at once, there was a factory amp that was not getting powered correctly. On my 2.3LX it was a silver amp mounted to the tranny tunnel behind the radio, but it may be found in various places.
That being said, a factory amp isn't really beneficial to your sound system if you have an aftermarket deck, so wiring around the amp is many times the best alternative. By re-wiring the speakers, you've effectively done this. For anyone else who may want to attempt this, there is a slightly easier way, you should be able to get your wires at the factory amp to go to the speaker (amp outputs). Just check continuity from those wires to the ones at your speakers and run them to your aftermarket deck.
The only way to check this is to have PJB check the impedance between the positive and negative terminals on his speakers (should be 2-4 ohms), or connect a 9V battery to the two terminals on the speakers (should drive the speaker in or out). If either one causes a change, the speakers were good...for a factory speaker anyway...
Figured I'd throw out what little wisdom I have for anyone else.
Kyle